Had To Choose
by xenowriter
Summary: John has to make a tough decision and the fallout is not what expects
1. Chapter 1

HAD TO CHOOSE

Part 1

John Shepard walked down the busy aisle of the Normandy towards the war room. His sunken eyelids on his face revealed the sleepless nights, the stubby hair on his chin displayed the disruption in the military standard routine of a clean shave. His jaw squared with his fists clenched by his sides. Despite the struggle, everything was coming together. Mordin contacted him at 0300 to advise a breakthrough in his research. Any Alliance offer would grumble in the disturbance of their sleep, but John was wide awake. He had been waiting for this call for several weeks now. It felt like months since obtaining Mordin and Eve from Surkesh and felt like years since he left San Francisco, Earth. Despite growing up on Alliance ships while his mother served, he still held attachment to Earth. It was humanity's homeworld. Families were scattered, scared, injured and fighting for their lives along with his best friend, Admiral David Anderson. Just like his marine comrade, James Vega, wanted, they needed to get back to Earth. Going at the Reapers alone was not an option. He required every species' assistance, but their home planets were being attacked. Backroom deals had to be made, politics to be played. He hated it. He wasn't born a politician and didn't have the patience to broker treaties. It wasn't his forte. Admiral Hackett depended on him. The Alliance depended on him. Earth depended on him. He went against odds before when he went up against Saren, The Geth and the Collectors. He could do it again.

Samantha Traynor caught his eye as he neared the war room door. "Commander Shepard, do you have a moment?"

"Not really, Specialist Traynor," Shepard stopped abruptly to address her concern. "What's this about?"

"I received reports that Grissom Academy is under attack by Cerberus. I also noticed that you have multiple messages in your inbox that have not been read. Did you want me to flag the ones that will be the most urgent to your private terminal in your quarters, sir?"

Grissom Academy's attack was alarming to John. Grissom was the Alliance funded biotic school for children. There was no logic behind Cerberus' attack on it right now. "What the hell is the Illusive Man up to?" He groaned. "I don't have time for this shit." Dealing with Cerberus was becoming an annoyance. There were several missions he took on due to Cerberus' random raids on Alliance stations that housed reaper tech and colonies. He could understand the need for reaper tech, since the Illusive Man had his eye on his own personal agenda with the artificial beings. The colonists were a mystery, and several were rescued while many were lost to the troops. He was close. So close to curing the genophage, the demand that Urdnot Wrex made to complete the deal between the krogan and the turians. The salarians wanted no part in the treaty. The Dalatrass felt that dealing with the krogan was unwise and ill advised. She openingly argued against it, bringing up the past krogan rebellion and the past need for the genophage. Wrex was John's friend and showed him more loyalty than the Dalatrass. He trusted the krogan leader. Earth's survival depended upon the treaty and there could be no further delays. "Flag the nearest Alliance vessel in the sector. Tell them about the distress signal and ask them to get there as soon as possible."

The order seemed to shock the young woman. "Uh, right, Commander," She stuttered as she moved back to her workstation to make contact.

John blocked out all the images of the poor students hiding away in their rooms as Cerberus soldiers moved in on the academy. This war was causing him to make tough decisions. He never wanted to see children involved in the crossfire. It was painful enough for the young child on Earth to be killed when their shuttle was taken out by a Reaper beam. The disturbing image haunted his dreams each time he closed his eyes. However, on Earth, hundreds of children were being killed by Reaper forces or dragged off to be turned into husks. At some point, he would deal with Cerberus. There was no need for the cruelty of the Illusive Man to slaughter children. There had to be a reason behind the attack on the academy. Shepard prayed that he would be right, and the leader of the pro human organization would keep them alive, and unharmed in some facility. Once the treaty was complete, then he would find them. Taking a deep breath, he lifted his blue eyes back towards the war room doors. "I have to choose."

"And your messages, sir?" Traynor called back to him.

Without turning around to acknowledge her once more, John replied, "I'll deal with them later."

Entering the war room, he saw Mordin, Wrex and the Primarch standing around a holo image of the shroud on Tuchanka. A smaller class Reaper stationed itself right in front to block off any attacks. The Reapers were onto them and they were ready to deflect the cure. Wrex looked his way as he entered. "About time you showed up, Shepard. You ready to do this?"

"You bet, Wrex. It's been a long time coming for your people."

"You can say that again," The burly krogan grumbled as he shifted his glance over to the Mordin. "You heard that, Pyjak?"

Mordin studied the image as his quick salarian mind with STG training tried to derive of a plan of strategy. "I did…the Reaper was unexpected." A beat. "Problematic."

Wrex chuckled. "Makes it more fun."


	2. Chapter 2

HAD TO CHOOSE: PART 2

A single breath exhaled from John's trembling lips as his right index finger slowly slipped off the monitor control panel. His entire body felt like it was going to go limp as if he was struck by a sedative injection. The hellish image that his mind depicted upon hearing the Cerberus recording on their present location played in a constant loop. He could see Jack strapped down to a metal examination table. Her body riddled with electrodes and wires as several Cerberus scientists stood over her, looking on with sadistic pleasure. Their lips twisted into wicked smiles as they saw their prey helpless once again at their mercy. Last time, Jack, aka Subject Zero, was a child on Pragia. She got the better of them then. This time, she would have no say in her fate. Her biotics disabled. They took all precautions once Cronos Station was prepped for arrival. In the darkened corner of the lab, John could almost see the Illusive Man intensively looking on. His glowing blue eyes lighting up his face. A hint of a chuckle of enjoyment escaped his mouth with the vapor from his cigarette. The screams of the students from Grissom Academy were faint as if the metal walls of the ship dampened their volume. Their young voices, petrified, with feign hope of someone other than Cerberus hearing their pleas of salvation. Thankfully, Shepard's imagination chose not to reroute him down the dark path to show what each child was enduring at Cerberus' discretion.

By the time the Alliance ship was inbound to Grissom, the station was deserted, and all its previous occupants were either dead in the hallways or taken away by the Cerberus troopers. Smoke and alarms were the only things that remained. The normal procedure would be to download all data and mine it to get a roster on who all was present, then scrub. Unfortunately, once the station was stabilized, the normal procedure was placed on hold and the Alliance left. The Reaper War caused all resources to be stretched thin and to put it simply, the Alliance didn't have time to carry out normal protocols. More colonies were being attacked at every corner either by Cerberus or the Reapers. It almost seemed like their attacks were a seamless transition into one. Was the Illusive Man onboard with the enemy? His talks with Shepard didn't show that he was going to bed with the enemy, but then again, he was the kind of person that would show you one hand, while hiding the other.

"Shepard," Garrus' voice broke all revelations.

"I don't need to hear it." John cut him off. His voice curter than he intended. His emotions running high. He lost contact with Jack after he was imprisoned by the Alliance for his alleged war crimes against the Batarian Hegemony. With the Reaper attack on Earth, his entire life was spun into chaos and it seemed like there was never a free moment to just sit down in his cabin and send messages out. Instead, his inbox was full of unread messages from desperate cries for help. Their senders hoping that once again, Commander Shepard would rush to their rescue. As of his previous missions against the Collectors were not in a time crunch as it was. He still found time to help those who needed him. This time, he had to ignore the requests or simply deny them. "I had to choose, and I will stand by my decision. Jack would have understood." A lump formed in his throat as he spoke out her ghostly name.

"Understood, Commander. I'm with you all the way." His turian friend gently reminded him, backing off from further discussion.

"We should get moving. The fleet will be hitting this place soon." Liara urged from where she stood on the right side of John.

"Not soon enough," John scowled as the words pushed their way through his gritted teeth. His fists clenched tightly as he forced himself away from the controls. A part of him wanted to search every room to find Jack or at least her body, but he knew time dictated their every step. Even if he did come across her, would he even like what he saw? Guarded, his heart begged him not to think about the touchy topic just yet. Was he and Jack that close? A few flirts aboard the Normandy as they pursued the Collectors and then one thing led to another. John came to Jack with urges, unable to withstand their beckoning further. Something about her, her fire, her attitude, made him long for her. He never came across a woman like her before. Then again, he never really had a desire to be involved with an ex-convict. They never took the step in saying how much they felt for each other and he wondered if their sexual encounters meant that the relationship was physical and not emotional. Though, the pain he was feeling currently made him realize that deep down the emotional aspect was there, yet never divulged to himself or her.

Regret hardened on his lips like cement and his mouth became dry. Why didn't he tell her how he felt? At least before he turned himself into the Alliance. He never told her he was going to face the charges against him. Jack didn't care if he blew up Aratoht. Like most humans, she disliked the batarian race and her run-ins with them in her earlier pirate days, were not pleasant ones. Par for the course. As he reflected upon this further briefly, he could almost hear her cussing him out about his decision and pressuring him to not turn himself in. He had no idea that she joined Grissom Academy. Why did she? It didn't fit her personality. What was in it for her? Was she hiding out from Cerberus? Was that the reason why they decided to strike the academy? Or was it pure luck that they almost stumbled upon Subject Zero once again. Another win for the Illusive Man.

"Let's move out." John gripped his assault rifle as he went through the lab doors first into the darkened halls once more. The station began to shake as violent impacts on the far starboard side could be heard echoing throughout the metal structure. The attack on Cronos had begun. Déjà vu. It was as if he was on the Geth Dreadnought all over again. "Why can't I ever leave a ship before someone else starts to destroy it?" He tossed out lightheartedly to his team. An attempt to clear up his foggy thoughts.

"Yeah, but unlike the Quarians, this time, we kind of know where they were hit first and give us time to get out of the way." Garrus commented behind him.

"I'm glad I wasn't there for that." Liara muttered following the pair.

A light up ahead revealed an open chamber of the station. Shepard's combat boots echoed along the metal catwalk as they entered the vast chamber. He began to wonder just how large this ship was. His jaw nearly dropped to the ground when he saw another ghost from his past come to his blue eyes. Hanging by mechanical metal arms was the skeleton remains of the human reaper he tangled with on the Collector ship. "Holy hell…."

Garrus' mandible twitched as the turian stopped along aside him to stare up at the hollowed eye artificially created being. "Is it turned on?"

"Goddess, what is that?" Liara's voice quivered.

John remembered that his asari comrade wasn't with him on their last suicide mission. "Figured that he would want that thing for himself." Referring to the Illusive Man and the conversation he had with him before deciding to keep the Collector ship intact for salvage. At the time, he was done dealing with the Illusive Man and didn't care what interest he had with it. The Collectors were dead as far as he was concerned, and his crew was rescued. The threat against colonists would be over. No more families taken aboard Collector ships, their bodies melted down into fluids for the construction of the human reaper. A sickening fate for anyone to endure.

Chattering ahead sprung their attention and their weapons at the ready. "Inbound!" Liara spoke out the already known.

John's arms tensed as he held the assault rifle closer to his chest, his trigger finger ready. "Bring it on…." He hissed. It was time for payback.

A bright glint from a sword grasped his focus and he saw a slim figure land acrobatically onto the platform ahead. It wasn't the first time they came across the engineered Cerberus Phantoms. "Commander!" Garrus alerted his attention to their old foe. The Phantoms were a great threat than the Nemesis or standard trooper. Unlike the others, the Phantom had a cloaking capability and their swords could pierce shields and armor plating.

Moving his sights towards the Phantom, John could hear his breath quickening as his adrenaline flowed. "I'll get you, you son-of-a-bitch."

"I will destroy you!" A familiar voice from the Phantom's direction shattered his focus.

Were his ears deceiving him? Blinking, John untensed and looked upon the mechanical being once again. "What…..." The Phantom was too far away to get a true visual of their appearance. His heart raced. He had to be wrong. He looked over to his squadmates and saw that Garrus was armed with his M-29 Incisor Sniper Rifle. "Zoom in on it!"

Without acknowledgement, Garrus switched his scope towards the Phantom to zero in on it. "That's not good…. ugh, Commander, we have a serious problem!"

The turian's heightened alarm confirmed what John already knew. "It's Jack…." Her name once again escaped his lips. His finger on the trigger shook with conflict. The sick bastard was going to force her death by his own hand.


End file.
